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question about evidence codes

Heather Butler hbutler at caprion.com
Wed Sep 12 08:41:53 PDT 2001


Hi Gillian,

If I have understood correcly then from:
> The experiment they did was to overexpress the oskar (osk) gene in the
> anterior of embryos in an otherwise wild-type background and you get
> ectopic pole cells at the anterior of the embryo (as well as 
> the normal
> ones at the posterior end).
> 
> They then make the embryos that are expressing osk anteriorly also
> mutant for aub and in these double mutant embryos they find that the
> ectopic pole cells are not formed.  This gives evidence that aub is
> required for the development of ectopic pole cells at the anterior of
> the embryo (evidence 1, IGI).

I would use:
*d pole cell formation ; GO:0007279 | IGI with FB:osk
as it can stand alone as a true statement.

I would not use the fact that aub is expressed in the pole cells as
evidence that aub is involved in the process of pole cell formation.
Expression pattern evidence like that is more for cellular component and
expression pattern is very rarely used as evidence for a process.

Is this helpful, or have I mis-understood (I read your email fairly
quickly!)?

Heather

> -----Original Message-----
> From: Gillian Millburn (Genetics) [mailto:gm119 at gen.cam.ac.uk]
> Sent: Wednesday, September 12, 2001 8:53 AM
> To: gofriends at geneontology.org
> Cc: gm119 at gen.cam.ac.uk
> Subject: question about evidence codes
> 
> 
> hello GO people,
> 
> I am trying to add a GO process term to my curation of a paper for
> FlyBase and I need some help.
> 
> The paper is:
> 
> Harris et al., 2001, Development 128(14): 2823--2832
> 
> which is about the aubergine (aub) gene.
> 
> The GO term I want to add is:
> 
> pole cell formation ; GO:0007279
> 
> but I am not sure what evidence code to add because of the way the
> experiment was done - they couldn't just look directly at pole cell
> formation in aub single mutants, because aub is required for efficient
> osk translation and osk itself is needed for pole cell formation, so
> the lack of pole cells in aub single mutants could be indirect due to
> its effect on osk translation.
> 
> The experiment they did was to overexpress the oskar (osk) gene in the
> anterior of embryos in an otherwise wild-type background and you get
> ectopic pole cells at the anterior of the embryo (as well as 
> the normal
> ones at the posterior end).
> 
> They then make the embryos that are expressing osk anteriorly also
> mutant for aub and in these double mutant embryos they find that the
> ectopic pole cells are not formed.  This gives evidence that aub is
> required for the development of ectopic pole cells at the anterior of
> the embryo (evidence 1, IGI).
> 
> They also showed by using a UAS-GFP-aub transgene that aub is a
> component of the polar granules (evidence 2, IEP)
> 
> The two evidences combined I think give enough evidence that aub is
> involved in formation of the (normal) posterior pole cells, 
> but I don't
> think that either evidence alone is enough to add the GO term above to
> the aub gene.
> 
> There is a bit in the GO evidence documentation which 
> suggests I should
> use TAS:
> 
> > Added 2000-11-08: Heather has seen cases where a paper presents
> > several lines of evidence supporting a conclusion, of which 
> each line
> > of evidence alone is sufficient to annotate to a higher-level (more
> > genric) node, but combining the lines of evidence gives the 
> author (or
> > curator) enough data to support annotating to a lower-level (more
> > specific) node. We've decided to annotate each line of evidence
> > singly, with the appropriate evidence code, for the higher node
> > (e.g. have a line for IMP, another line for IPI, for one GO ID). The
> > annotation to the lower node can then be included with 'TAS' as the
> > evidence; cite the paper if the author draws the conclusion. If the
> > curator draws the conclusion, keep some record of what went into the
> > decision.
> 
> 
> so I could add:
> 
> pole cell formation ; GO:0007279 | TAS
> 
> but in this case there isn't really a higer level (more 
> general) term I
> could add with the IGI or IEP evidences. If I only put the 
> above line I
> will lose information.
> 
> Could you clarify whether if a GO term is added with a single piece of
> evidence, e.g.:
> 
> pole cell formation ; GO:0007279 | IGI with FB:osk
> pole cell formation ; GO:0007279 | IEP
> 
> that the implication is that the single type of evidence alone is
> enough to assign the GO term - if that is the case then I cannot add
> the above 2 GO terms to aub because I don't think its true - you need
> both of them combined, but if I don't put the above 2 GO 
> terms and only
> put the TAS one then I lose info, help !!
> 
> Gillian
> 
> --------------------------------------------------------------
> Gillian Millburn.
> 
> FlyBase (Cambridge),
> Department of Genetics,
> University of Cambridge,
> Downing Street,                       email: gm119 at gen.cam.ac.uk
> Cambridge,  CB2 3EH,                  Ph : 01223-333963
> UK.                                   FAX: 01223-333992
> --------------------------------------------------------------
> 
> 
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